Improve performance of element handling

[baoilleach]

As described over at openbabel/enhancement-proposals#4.

Briefly, the old element handling code had some performance problems. I have written a faster replacement. It has the following additional benefits:

1. No need for a global etab or isotab and associated initialization.
2. The elements are now available as consts (e.g. OBElements::Carbon) to replace functions such as IsCarbon().
3. No need for text/header files in data dir.

Timing comparison: get the symbol for elements 1 to 100 and convert back to atomic number (repeat x10000). 0.82s old vs 0.02s new. A more realistic conversion is to just do carbon: 0.14s old vs 0.01s new.

void test_OBElements()
{
  clock_t start = clock();
  unsigned int tot = 0;
  for (unsigned int N = 0; N < 10000; ++N) {
    for (unsigned int i = 1; i < 100; ++i) {
      const char *elem = OBElements::GetSymbol(6);
      unsigned int atomic_num = OBElements::GetAtomicNum(elem);
      tot += atomic_num;
    }
  }
  clock_t stop = clock();
  double sum = (double)(stop - start) / CLOCKS_PER_SEC;
  printf("%.2f s\n", sum);
  
  OBElementTable etab;
  start = clock();
  tot = 0;
  for (unsigned int N = 0; N < 10000; ++N) {
    for (unsigned int i = 1; i < 100; ++i) {
      const char *elem = etab.GetSymbol(6);
      unsigned int atomic_num = etab.GetAtomicNum(elem);
      tot += atomic_num;
    }
  }
  stop = clock();
  sum = (double)(stop - start) / CLOCKS_PER_SEC;
  printf("%.2f s\n", sum);
}

[baoilleach]

Updated timings, for the record, with 3 signif figures and 10x more iterations:

Timing comparison: get the symbol for elements 1 to 100 and convert back to atomic number (repeat x100000). 8.05s old vs 0.187s new. A more realistic conversion is to just do carbon: 1.34s old vs 0.078s new.

[baoilleach]

Good to merge? Or not...?

[ghutchis]

Yep, it looks good. Sorry for the delay

[n-yoshikawa]

Could you show me how to use OBElements in Python binding?
For example, how can I replace the following code?

import openbabel

etab = openbabel.OBElementTable()
print(etab.GetSymbol(6))

[baoilleach]

https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#handling-of-elements-and-related-information

…

On Sun, 9 Jun 2019, 09:40 Naruki Yoshikawa, ***@***.***> wrote: Could you show me how to use OBElements in Python binding? For example, how can I replace the following code? import openbabel etab = openbabel.OBElementTable()print(etab.GetSymbol(6)) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1601?email_source=notifications&email_token=AAALCGIO35247YSN4P4PXBTPZS6YVA5CNFSM4DS2IKEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXIGFSY#issuecomment-500196043>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAALCGOZ5ZS4BQMBAPYU5QDPZS6YVANCNFSM4DS2IKEA> .

[n-yoshikawa]

I tried the following test.py in the current master,

from openbabel import openbabel
  
print(openbabel.OBElements.GetSymbol(6))

but it yielded the followng error.

$ python3 test.py 
Traceback (most recent call last):
  File "test.py", line 3, in <module>
    print(openbabel.OBElements.GetSymbol(6))
AttributeError: module 'openbabel.openbabel' has no attribute 'OBElements'

[baoilleach]

Just GetSymbol will work without the OBElements.

…

On Sun, 9 Jun 2019, 10:30 Naruki Yoshikawa, ***@***.***> wrote: I tried the following test.py in the current master, from openbabel import openbabel print(openbabel.OBElements.GetSymbol(6)) but it yielded the followng error. $ python3 test.py Traceback (most recent call last): File "test.py", line 3, in <module> print(openbabel.OBElements.GetSymbol(6)) AttributeError: module 'openbabel.openbabel' has no attribute 'OBElements' — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1601?email_source=notifications&email_token=AAALCGIMJBQYZF7WH4HAFBLPZTETHA5CNFSM4DS2IKEKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODXIGZPI#issuecomment-500198589>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAALCGODS2U3OMT37K6KUVTPZTETHANCNFSM4DS2IKEA> .